Mercury (Hg) is a global environmental pollutant that has been the cause of many public concerns. One particular concern about Hg in aquatic systems is its trophic transfer and biomagnification in food chains. For example, the Hg concentration increases with the increase of food chain level. Fish at the top of food chain can accumulate high concentrations of Hg (especially the toxic form, methylmercury, MeHg), which is then transferred to humans through seafood consumption. Various biological and hysiochemical conditions can significantly affect the bioaccumulation of Hg−including both its inorganic (Hg(II)) and organic (MeHg) forms−in fish. There have been numerous measurements of Hg concentrations in marine and freshwater fish worldwide. Many of these studies have attempted to identify the processes leading to variations of Hg concentrations in fish species from different habitats. The development of a biokinetic model over the past decade has helped improve our understanding of the mechanisms underlying the bioaccumulation processes of Hg in aquatic animals. In this review, I will discuss how the biokinetic modeling approach can be used to reveal the interesting biodynamics of Hg in fish, such as the trophic transfer and exposure route of Hg(II) and MeHg, as well as growth enrichment (the increases in Hg concentration with fish size) and biomass dilution (the decreases in Hg concentration with increasing phytoplankton biomass). I will also discuss the relevance of studying the subcellular fates of Hg to predict the Hg bioaccessibility and detoxification in fish. Future challenges will be to understand the inter- and intra-species differences in Hg accumulation and the management/mitigation of Hg pollution in both marine and freshwater fish based on our knowledge of Hg biodynamics.